Package edu.cmu.tetrad.algcomparison.algorithm.oracle.pag

Class SpFci

java.lang.Object

edu.cmu.tetrad.algcomparison.algorithm.AbstractBootstrapAlgorithm

edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SpFci

All Implemented Interfaces:

Algorithm, ReturnsBootstrapGraphs, TakesCovarianceMatrix, HasKnowledge, HasParameters, TakesIndependenceWrapper, UsesScoreWrapper, TetradSerializable, Serializable

@Algorithm(name="SP-FCI",
           command="spfci",
           algoType=allow_latent_common_causes)
@Bootstrapping
public class SpFci
extends AbstractBootstrapAlgorithm
implements Algorithm, UsesScoreWrapper, TakesIndependenceWrapper, HasKnowledge, ReturnsBootstrapGraphs, TakesCovarianceMatrix

Adjusts GFCI to use a permutation algorithm (in this case SP) to do the initial steps of finding adjacencies and unshielded colliders.

GFCI reference is this:

J.M. Ogarrio and P. Spirtes and J. Ramsey, "A Hybrid Causal Search Algorithm for Latent Variable Models," JMLR 2016.

Version:

$Id: $Id

Author:

josephramsey

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
SpFci()	The SpFci class represents a specific algorithm for structural learning called "Conditional Independence Test-based Fast Causal Inference" (SpFci).
SpFci(IndependenceWrapper test, ScoreWrapper score)	Constructor for the SpFci class.

Method Summary

Modifier and Type	Method	Description
Graph	getComparisonGraph(Graph graph)	Returns the comparison graph created by converting a true directed graph into a partially directed acyclic graph (PAG).
DataType	getDataType()	Returns the data type that the search requires, whether continuous, discrete, or mixed.
String	getDescription()	Returns a short, one-line description of this algorithm.
IndependenceWrapper	getIndependenceWrapper()	Retrieves the IndependenceWrapper associated with this algorithm.
Knowledge	getKnowledge()	Retrieves the knowledge object associated with this algorithm.
List<String>	getParameters()	Returns the list of parameters used by the method.
ScoreWrapper	getScoreWrapper()	Retrieves the ScoreWrapper object associated with this algorithm.
Graph	runSearch(DataModel dataModel, Parameters parameters)	Executes a search algorithm to infer the causal graph structure from a given data model
void	setIndependenceWrapper(IndependenceWrapper test)	Sets the IndependenceWrapper object for the algorithm.
void	setKnowledge(Knowledge knowledge)	Sets the knowledge object associated with this algorithm.
void	setScoreWrapper(ScoreWrapper score)	Sets the ScoreWrapper object for the algorithm.

Methods inherited from class edu.cmu.tetrad.algcomparison.algorithm.AbstractBootstrapAlgorithm

getBootstrapGraphs, search

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface edu.cmu.tetrad.algcomparison.algorithm.Algorithm

search

Methods inherited from interface edu.cmu.tetrad.algcomparison.algorithm.ReturnsBootstrapGraphs

getBootstrapGraphs

Constructor Details

SpFci

public SpFci()

The SpFci class represents a specific algorithm for structural learning called "Conditional Independence Test-based Fast Causal Inference" (SpFci). This class extends the AbstractBootstrapAlgorithm class and implements the Algorithm, UsesScoreWrapper, and TakesIndependenceWrapper interfaces.

SpFci

public SpFci(IndependenceWrapper test,
 ScoreWrapper score)

Constructor for the SpFci class.

Parameters:

test - The IndependenceWrapper object to be used for the algorithm.

score - The ScoreWrapper object to be used for the algorithm.

Method Details

runSearch

public Graph runSearch(DataModel dataModel,
 Parameters parameters)
                throws InterruptedException

Executes a search algorithm to infer the causal graph structure from a given data model

Parameters:

dataModel - The data model representing the observed variables and their relationships

parameters - The parameters for the search algorithm

Returns:

The inferred causal graph structure

Throws:

InterruptedException

getComparisonGraph

public Graph getComparisonGraph(Graph graph)

Returns the comparison graph created by converting a true directed graph into a partially directed acyclic graph (PAG).

Specified by:

getComparisonGraph in interface Algorithm

Parameters:

graph - The true, directed graph, if there is one.

Returns:

The comparison graph as a partially directed acyclic graph (PAG).

getDescription

public String getDescription()

Returns a short, one-line description of this algorithm. This will be printed in the report.

Specified by:

getDescription in interface Algorithm

Returns:

The description of this algorithm.

getDataType

public DataType getDataType()

Returns the data type that the search requires, whether continuous, discrete, or mixed.

Specified by:

getDataType in interface Algorithm

Returns:

The DataType of this algorithm.

getParameters

public List<String> getParameters()

Returns the list of parameters used by the method.

Specified by:

getParameters in interface HasParameters

Returns:

A List of strings representing the parameters used by the method.

getKnowledge

public Knowledge getKnowledge()

Retrieves the knowledge object associated with this algorithm.

Specified by:

getKnowledge in interface HasKnowledge

Returns:

The knowledge object.

setKnowledge

public void setKnowledge(Knowledge knowledge)

Sets the knowledge object associated with this algorithm.

Specified by:

setKnowledge in interface HasKnowledge

Parameters:

knowledge - The knowledge object to be set.

getIndependenceWrapper

public IndependenceWrapper getIndependenceWrapper()

Retrieves the IndependenceWrapper associated with this algorithm.

Specified by:

getIndependenceWrapper in interface TakesIndependenceWrapper

Returns:

The IndependenceWrapper object.

setIndependenceWrapper

public void setIndependenceWrapper(IndependenceWrapper test)

Sets the IndependenceWrapper object for the algorithm.

Specified by:

setIndependenceWrapper in interface TakesIndependenceWrapper

Parameters:

test - the IndependenceWrapper object to be set.

getScoreWrapper

public ScoreWrapper getScoreWrapper()

Retrieves the ScoreWrapper object associated with this algorithm.

Specified by:

getScoreWrapper in interface UsesScoreWrapper

Returns:

The ScoreWrapper object.

setScoreWrapper

public void setScoreWrapper(ScoreWrapper score)

Sets the ScoreWrapper object for the algorithm.

Specified by:

setScoreWrapper in interface UsesScoreWrapper

Parameters:

score - the score wrapper.